VMD-L Mailing List

From: Vyom Sharma (vysharma_at_MIT.EDU)
Date: Thu Jun 01 2006 - 17:34:04 CDT

I am getting a very strange problem for quite sometime now.
I use a "PQR" file that i generate and run it on APBS to give me the
potential data.
VMD is able to show the molecule nicely but it is not able to visualize
the potential data at all. Infact it does not show anything when I try
to load the potential data.

I am using the "my_functions" script to sort and load the potential
data into VMD.
Also I am attaching the "PQR" file (I can send the "pot.dx" file which
contains the potential data , if required- its 27 MB big)

While loading the potential using "load_pot" command, I get these
messages:

---------------------
nfo) VMD for MACOSX, version 1.8.4 (April 17, 2006)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 1 CPU detected.
Info) OpenGL renderer: ATI Radeon 9200 OpenGL Engine
Info) Features: STENCIL MTX
Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (6)
vmd > source my_functions
vmd > load_pot
Info) Using plugin pdb for structure file sphere.pqr
Info) Using plugin pdb for coordinates from file sphere.pqr
Info) Determining bond structure from distance search ...
ERROR) MolAtom 131: Exceeded maximum number of bonds (8).
ERROR) MolAtom 173: Exceeded maximum number of bonds (8).
ERROR) MolAtom 285: Exceeded maximum number of bonds (8).
ERROR) MolAtom 423: Exceeded maximum number of bonds (8).
ERROR) MolAtom 79: Exceeded maximum number of bonds (8).
ERROR) MolAtom 310: Exceeded maximum number of bonds (8).
ERROR) MolAtom 147: Exceeded maximum number of bonds (8).
ERROR) MolAtom 475: Exceeded maximum number of bonds (8).
ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
ERROR) MolAtom 292: Exceeded maximum number of bonds (8).
ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
ERROR) MolAtom 256: Exceeded maximum number of bonds (8).
ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
ERROR) MolAtom 210: Exceeded maximum number of bonds (8).
ERROR) MolAtom 110: Exceeded maximum number of bonds (8).
ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps atom
coordinates are in the wrong units?
ERROR) BaseMolecule: Silencing bonding error messages.
Info) Finished with coordinate file sphere.pqr.
Info) Analyzing structure ...
Info) Atoms: 501
Info) Bonds: 1112
Info) Residues: 53
Info) Waters: 0
---------------------------------------

I would immensely appreciate any repsonse.

Thanks
Vyom